title: Identification of novel CR1 subfamilies in an avian order with recently active elements.
abstract: Chicken repeat 1 (CR1) is a taxonomically widespread non-LTR retrotransposon. Recent CR1 retrotranspositions in waterfowl suggested that, unlike chicken at least one subfamily remains active. Based on sequence information from 143 CR1 loci, six distinct groups of CR1 within the waterfowl coscoroba each with unique 3' untranslated regions and distinct open reading frames are described. Through comparison to other previously described avian CR1 subfamilies, it is shown that five of the six coscoroba groups represent new subfamilies. At least one of these subfamilies is likely active and provides a target for future isolation of the first active member of this taxonomically widespread non-LTR family.
authors.affiliation: Rocky Mountain Center for Conservation Genetics and Systematics, Department of Biological Sciences, University of Denver, 2190 E Iliff Ave., Denver, CO 80208, USA. jstjohn@du.edu
authors.forename: Judy
authors.initials: J
authors.lastname: St John
authors.forename: Thomas W
authors.initials: TW
authors.lastname: Quinn
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics; D000818:Animals; D046090:Anseriformes / Q000235:genetics*; D001483:Base Sequence; D001499:Bayes Theorem; D002645:Chickens / Q000235:genetics*; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D018626:Retroelements; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D020413:3' Untranslated Regions; D018626:Retroelements